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Rosetta
2020.50
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#include <RotamerTrialsMover.hh>
Public Types | |
typedef core::scoring::ScoreFunctionOP | ScoreFunctionOP |
typedef core::scoring::ScoreFunctionCOP | ScoreFunctionCOP |
typedef core::pack::task::PackerTask | PackerTask |
typedef core::pack::task::PackerTaskOP | PackerTaskOP |
typedef core::pack::task::PackerTaskCOP | PackerTaskCOP |
typedef core::pack::task::TaskFactoryCOP | TaskFactoryCOP |
typedef protocols::moves::MoverOP | MoverOP |
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typedef utility::tag::TagCOP | TagCOP |
typedef core::pose::Pose | Pose |
typedef core::pose::PoseCOP | PoseCOP |
typedef std::list< std::string > | Strings |
Public Member Functions | |
RotamerTrialsMover () | |
RotamerTrialsMover (ScoreFunctionCOP scorefxn_in, PackerTask &task_in) | |
constructor with PackerTask. use a PackerTask ONLY for fixed-sequence work. WARNING TO ANY DESIGNER WHO PASSES IN A TASK: YOUR DESIGN STEPS WILL BE UNDONE AS THIS TASK CONCEIVES OF THE INPUT SEQUENCE THAT CORRESPONDS TO THE ORIGINAL SEQUENCE More... | |
RotamerTrialsMover (ScoreFunctionCOP scorefxn_in, TaskFactoryCOP factory_in) | |
constructor with TaskFactory More... | |
RotamerTrialsMover (RotamerTrialsMover const &rval) | |
copy constructor More... | |
~RotamerTrialsMover () override | |
destructor More... | |
protocols::moves::MoverOP | clone () const override |
clone this object More... | |
protocols::moves::MoverOP | fresh_instance () const override |
create this type of object More... | |
void | apply (core::pose::Pose &pose) override |
Main Method. More... | |
void | show (std::ostream &output=std::cout) const override |
Outputs details about the Mover, including current settings. More... | |
void | score_function (core::scoring::ScoreFunctionCOP sf) |
void | task_factory (core::pack::task::TaskFactoryCOP tf) |
void | parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override |
parse xml More... | |
std::string | get_name () const override |
Each derived class must specify its name. The class name. More... | |
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Mover () | |
virtual MoverOP | create () |
MoverCOP | get_self_ptr () const |
MoverOP | get_self_ptr () |
MoverCAP | get_self_weak_ptr () const |
MoverAP | get_self_weak_ptr () |
Mover (std::string const &type_name) | |
sets the type for a mover; name_ has been removed (2010/05/14) More... | |
virtual void | test_move (Pose &pose) |
: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More... | |
virtual bool | reinitialize_for_each_job () const |
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More... | |
virtual bool | reinitialize_for_new_input () const |
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More... | |
MoverStatus | get_last_move_status () const |
end parser interface, start Job Distributor interface///////////// More... | |
void | reset_status () |
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More... | |
virtual core::pose::PoseOP | get_additional_output () |
Mechanism by which a mover may return multiple output poses from a single input pose. More... | |
void | set_type (std::string const &setting) |
Set the 'type' string. More... | |
std::string | get_type () const |
void | type (const std::string &type_in) |
Set the 'type' string. More... | |
std::string const & | type () const |
Get the set 'type' string. More... | |
virtual void | set_input_pose (PoseCOP pose) |
setter for poses contained for rms More... | |
virtual void | set_native_pose (PoseCOP pose) |
setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More... | |
PoseCOP | get_input_pose () const |
PoseCOP | get_native_pose () const |
void | set_current_job (protocols::jobdist::BasicJobCOP job) |
jobdist::BasicJobCOP | get_current_job () const |
virtual void | set_current_tag (std::string const &new_tag) |
std::string | get_current_tag () const |
A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More... | |
virtual core::Real | last_proposal_density_ratio () |
virtual void | clear_info () |
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More... | |
virtual Strings & | info () |
non-const accessor More... | |
virtual Strings const & | info () const |
const accessor More... | |
virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Static Public Member Functions | |
static std::string | mover_name () |
static utility::tag::XMLSchemaComplexTypeGeneratorOP | complex_type_generator_for_rotamer_trials_mover (utility::tag::XMLSchemaDefinition &xsd) |
static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
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static std::string | name () |
static void | register_options () |
Overload this static method if you access options within the mover. More... | |
Protected Member Functions | |
ScoreFunctionCOP | scorefxn () const |
read access for derived classes More... | |
PackerTaskCOP | task (core::pose::Pose const &pose) const |
read access for derived classes, pose needed to run TaskFactory More... | |
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void | set_last_move_status (MoverStatus status) |
nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More... | |
Private Attributes | |
ScoreFunctionCOP | scorefxn_ |
RotamerTrailsMover does not have its own score function, rather, it shares one with other classes – CAUTION: the score function is externally modifiable. More... | |
PackerTaskOP | task_ |
use a PackerTask ONLY for fixed-sequence work. WARNING TO ANY DESIGNER WHO PASSES IN A TASK: YOUR DESIGN STEPS WILL BE UNDONE AS THIS TASK CONCEIVES OF THE INPUT SEQUENCE THAT CORRESPONDS TO THE ORIGINAL SEQUENCE If a factory is present it overwrites this task with each call to apply() More... | |
TaskFactoryCOP | factory_ |
TaskFactory allows for nonconstant sequences to be used with RotamerTrialsMover CAUTION: the factory is externally modifiable. More... | |
bool | show_packer_task_ |
showing contents of PackerTask ( default false ) More... | |
typedef core::pack::task::PackerTask protocols::minimization_packing::RotamerTrialsMover::PackerTask |
typedef core::pack::task::PackerTaskCOP protocols::minimization_packing::RotamerTrialsMover::PackerTaskCOP |
typedef core::pack::task::PackerTaskOP protocols::minimization_packing::RotamerTrialsMover::PackerTaskOP |
typedef core::scoring::ScoreFunctionCOP protocols::minimization_packing::RotamerTrialsMover::ScoreFunctionCOP |
typedef core::scoring::ScoreFunctionOP protocols::minimization_packing::RotamerTrialsMover::ScoreFunctionOP |
typedef core::pack::task::TaskFactoryCOP protocols::minimization_packing::RotamerTrialsMover::TaskFactoryCOP |
protocols::minimization_packing::RotamerTrialsMover::RotamerTrialsMover | ( | ) |
References protocols::moves::Mover::type().
protocols::minimization_packing::RotamerTrialsMover::RotamerTrialsMover | ( | ScoreFunctionCOP | scorefxn_in, |
PackerTask & | task_in | ||
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constructor with PackerTask. use a PackerTask ONLY for fixed-sequence work. WARNING TO ANY DESIGNER WHO PASSES IN A TASK: YOUR DESIGN STEPS WILL BE UNDONE AS THIS TASK CONCEIVES OF THE INPUT SEQUENCE THAT CORRESPONDS TO THE ORIGINAL SEQUENCE
References core::pack::task::PackerTask::clone(), task_, and protocols::moves::Mover::type().
protocols::minimization_packing::RotamerTrialsMover::RotamerTrialsMover | ( | ScoreFunctionCOP | scorefxn_in, |
TaskFactoryCOP | factory_in | ||
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constructor with TaskFactory
References protocols::moves::Mover::type().
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default |
copy constructor
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overridedefault |
destructor
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overridevirtual |
Main Method.
Implements protocols::moves::Mover.
Reimplemented in protocols::minimization_packing::EnergyCutRotamerTrialsMover.
References core::pose::symmetry::is_symmetric(), core::pack::make_symmetric_task(), core::pack::rotamer_trials(), scorefxn_, show_packer_task_, core::pack::symmetric_rotamer_trials(), task(), and protocols::minimization_packing::TR().
Referenced by protocols::protein_interface_design::filters::FilterScanFilter::single_substitution().
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overridevirtual |
clone this object
Reimplemented from protocols::moves::Mover.
Referenced by protocols::minimization_packing::EnergyCutRotamerTrialsMover::apply().
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static |
References core::scoring::attributes_for_parse_score_function(), core::pack::task::attributes_for_parse_task_operations(), and protocols::moves::complex_type_name_for_mover().
Referenced by protocols::minimization_packing::symmetry::SymRotamerTrialsMover::provide_xml_schema(), and provide_xml_schema().
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overridevirtual |
create this type of object
Reimplemented from protocols::moves::Mover.
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overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
Reimplemented in protocols::minimization_packing::EnergyCutRotamerTrialsMover, protocols::minimization_packing::symmetry::SymEnergyCutRotamerTrialsMover, and protocols::minimization_packing::symmetry::SymRotamerTrialsMover.
References mover_name().
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static |
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overridevirtual |
parse xml
Reimplemented from protocols::moves::Mover.
References core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), scorefxn_, show_packer_task_, and task_factory().
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static |
void protocols::minimization_packing::RotamerTrialsMover::score_function | ( | core::scoring::ScoreFunctionCOP | sf | ) |
References scorefxn_.
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protected |
read access for derived classes
References scorefxn_.
Referenced by protocols::minimization_packing::EnergyCutRotamerTrialsMover::apply(), and show().
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overridevirtual |
Outputs details about the Mover, including current settings.
Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.
Reimplemented from protocols::moves::Mover.
References scorefxn().
Referenced by protocols::minimization_packing::operator<<().
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protected |
read access for derived classes, pose needed to run TaskFactory
read access for derived classes
References factory_, and task_.
Referenced by apply(), and protocols::minimization_packing::EnergyCutRotamerTrialsMover::apply().
void protocols::minimization_packing::RotamerTrialsMover::task_factory | ( | core::pack::task::TaskFactoryCOP | tf | ) |
References factory_.
Referenced by parse_my_tag().
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private |
TaskFactory allows for nonconstant sequences to be used with RotamerTrialsMover CAUTION: the factory is externally modifiable.
Referenced by task(), and task_factory().
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private |
RotamerTrailsMover does not have its own score function, rather, it shares one with other classes – CAUTION: the score function is externally modifiable.
Referenced by apply(), parse_my_tag(), score_function(), and scorefxn().
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private |
showing contents of PackerTask ( default false )
Referenced by apply(), and parse_my_tag().
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private |
use a PackerTask ONLY for fixed-sequence work. WARNING TO ANY DESIGNER WHO PASSES IN A TASK: YOUR DESIGN STEPS WILL BE UNDONE AS THIS TASK CONCEIVES OF THE INPUT SEQUENCE THAT CORRESPONDS TO THE ORIGINAL SEQUENCE If a factory is present it overwrites this task with each call to apply()
Referenced by RotamerTrialsMover(), and task().